Mercurial > repos > galaxyp > uniprotxml_downloader
comparison uniprotxml_downloader.xml @ 5:265c35540faa draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
author | galaxyp |
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date | Fri, 04 Nov 2022 15:08:37 +0000 |
parents | 12692567c7f9 |
children | a371252a2cf6 |
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4:12692567c7f9 | 5:265c35540faa |
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1 <tool id="uniprotxml_downloader" name="UniProt" version="2.2.0" profile="21.01"> | 1 <tool id="uniprotxml_downloader" name="UniProt" version="2.3.0" profile="21.01"> |
2 <description>download proteome as XML or fasta</description> | 2 <description>download proteome as XML or fasta</description> |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
3 <requirements> | 6 <requirements> |
4 <requirement type="package" version="2.25.1">requests</requirement> | 7 <requirement type="package" version="2.25.1">requests</requirement> |
5 </requirements> | 8 </requirements> |
6 <stdio> | 9 <stdio> |
7 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> | 10 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> |
9 <command> | 12 <command> |
10 <![CDATA[ | 13 <![CDATA[ |
11 python '$__tool_directory__/uniprotxml_downloader.py' | 14 python '$__tool_directory__/uniprotxml_downloader.py' |
12 #if $taxid.input_choice == 'common': | 15 #if $taxid.input_choice == 'common': |
13 --taxon $taxid.organism | 16 --taxon $taxid.organism |
17 --field taxonomy_id | |
14 #if $taxid.reviewed: | 18 #if $taxid.reviewed: |
15 --reviewed=$taxid.reviewed | 19 --reviewed=$taxid.reviewed |
16 #end if | 20 #end if |
17 #elif $taxid.input_choice == 'taxids': | 21 #elif $taxid.input_choice == 'taxids': |
22 --field $taxid.field | |
18 #for $id in $taxid.taxons.split(','): | 23 #for $id in $taxid.taxons.split(','): |
19 -t '$id' | 24 -t '$id' |
20 #end for | 25 #end for |
21 #elif $taxid.input_choice == 'history': | 26 #elif $taxid.input_choice == 'history': |
27 --field $taxid.field | |
22 --input='${taxid.taxon_file}' | 28 --input='${taxid.taxon_file}' |
23 --column=#echo int(str($taxid.column)) - 1# | 29 --column=#echo int(str($taxid.column)) - 1# |
24 #end if | 30 #end if |
25 --format $format | 31 --format $format |
26 --output '${proteome}' | 32 --output '${proteome}' |
56 <when value="taxids"> | 62 <when value="taxids"> |
57 <param name="taxons" type="text" label="NCBI Taxon IDs or names" | 63 <param name="taxons" type="text" label="NCBI Taxon IDs or names" |
58 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> | 64 help="Enter one or more Organsim IDs (separated by commas) from http://www.uniprot.org/proteomes/"> |
59 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> | 65 <validator type="regex" message="OrganismID[,OrganismID]">^\w+( \w+)*(,\w+( \w+)*)*$</validator> |
60 </param> | 66 </param> |
67 <expand macro="query_field"/> | |
61 </when> | 68 </when> |
62 <when value="history"> | 69 <when value="history"> |
63 <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/> | 70 <param name="taxon_file" type="data" format="tabular,txt" label="Dataset (tab separated) with Taxon ID/Name column"/> |
64 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/> | 71 <param name="column" type="data_column" data_ref="taxon_file" label="Column with Taxon ID/name"/> |
72 <expand macro="query_field"/> | |
65 </when> | 73 </when> |
66 </conditional> | 74 </conditional> |
67 <param name="format" type="select" label="uniprot output format"> | 75 <param name="format" type="select" label="uniprot output format"> |
68 <option value="xml">xml</option> | 76 <option value="xml">xml</option> |
69 <option value="fasta">fasta</option> | 77 <option value="fasta">fasta</option> |
87 </assert_contents> | 95 </assert_contents> |
88 </output> | 96 </output> |
89 </test> | 97 </test> |
90 <test> | 98 <test> |
91 <param name="input_choice" value="taxids"/> | 99 <param name="input_choice" value="taxids"/> |
100 <param name="taxons" value="765963,512562"/> | |
101 <param name="field" value="taxonomy_id"/> | |
102 <param name="format" value="fasta"/> | |
103 <output name="proteome"> | |
104 <assert_contents> | |
105 <has_text text="Shi470" /> | |
106 <has_text text="PeCan4" /> | |
107 </assert_contents> | |
108 </output> | |
109 </test> | |
110 <test> | |
111 <param name="input_choice" value="taxids"/> | |
92 <param name="taxons" value="Shi470,PeCan4"/> | 112 <param name="taxons" value="Shi470,PeCan4"/> |
113 <param name="field" value="taxonomy_name"/> | |
93 <param name="format" value="fasta"/> | 114 <param name="format" value="fasta"/> |
94 <output name="proteome"> | 115 <output name="proteome"> |
95 <assert_contents> | 116 <assert_contents> |
96 <has_text text="Shi470" /> | 117 <has_text text="Shi470" /> |
97 <has_text text="PeCan4" /> | 118 <has_text text="PeCan4" /> |
100 </test> | 121 </test> |
101 <test> | 122 <test> |
102 <param name="input_choice" value="history"/> | 123 <param name="input_choice" value="history"/> |
103 <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> | 124 <param name="taxon_file" value="Helicobacter_strains.tsv" ftype="tabular"/> |
104 <param name="column" value="1"/> | 125 <param name="column" value="1"/> |
126 <param name="field" value="taxonomy_name"/> | |
105 <param name="format" value="fasta"/> | 127 <param name="format" value="fasta"/> |
106 <output name="proteome"> | 128 <output name="proteome"> |
107 <assert_contents> | 129 <assert_contents> |
108 <has_text text="Shi470" /> | 130 <has_text text="Shi470" /> |
109 <has_text text="PeCan4" /> | 131 <has_text text="PeCan4" /> |
112 </test> | 134 </test> |
113 <test> | 135 <test> |
114 <param name="input_choice" value="history"/> | 136 <param name="input_choice" value="history"/> |
115 <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> | 137 <param name="taxon_file" value="Helicobacter_strains_ids.tsv" ftype="tabular"/> |
116 <param name="column" value="2"/> | 138 <param name="column" value="2"/> |
139 <param name="field" value="taxonomy_id"/> | |
117 <param name="format" value="fasta"/> | 140 <param name="format" value="fasta"/> |
118 <output name="proteome"> | 141 <output name="proteome"> |
119 <assert_contents> | 142 <assert_contents> |
120 <has_text text="Shi470" /> | 143 <has_text text="Shi470" /> |
121 <has_text text="PeCan4" /> | 144 <has_text text="PeCan4" /> |